| 1. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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| 2. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 3. |
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| 4. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 5. |
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| 6. |
- Gerkin, RC, et al.
(författare)
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The best COVID-19 predictor is recent smell loss: a cross-sectional study
- 2020
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Ingår i: medRxiv : the preprint server for health sciences. - : Cold Spring Harbor Laboratory.
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- BackgroundCOVID-19 has heterogeneous manifestations, though one of the most common symptoms is a sudden loss of smell (anosmia or hyposmia). We investigated whether olfactory loss is a reliable predictor of COVID-19.MethodsThis preregistered, cross-sectional study used a crowdsourced questionnaire in 23 languages to assess symptoms in individuals self-reporting recent respiratory illness. We quantified changes in chemosensory abilities during the course of the respiratory illness using 0-100 visual analog scales (VAS) for participants reporting a positive (C19+; n=4148) or negative (C19-; n=546) COVID-19 laboratory test outcome. Logistic regression models identified singular and cumulative predictors of COVID-19 status and post-COVID-19 olfactory recovery.ResultsBoth C19+ and C19-groups exhibited smell loss, but it was significantly larger in C19+ participants (mean±SD, C19+: -82.5±27.2 points; C19-: -59.8±37.7). Smell loss during illness was the best predictor of COVID-19 in both single and cumulative feature models (ROC AUC=0.72), with additional features providing negligible model improvement. VAS ratings of smell loss were more predictive than binary chemosensory yes/no-questions or other cardinal symptoms, such as fever or cough. Olfactory recovery within 40 days was reported for ∼50% of participants and was best predicted by time since illness onset.ConclusionsAs smell loss is the best predictor of COVID-19, we developed the ODoR-19 tool, a 0-10 scale to screen for recent olfactory loss. Numeric ratings ≤2 indicate high odds of symptomatic COVID-19 (4<OR<10), which can be deployed when viral lab tests are impractical or unavailable.
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| 7. |
- Lopes-Lima, M., et al.
(författare)
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Integrative phylogenetic, phylogeographic and morphological characterisation of the Unio crassus species complex reveals cryptic diversity with important conservation implications
- 2024
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Ingår i: Molecular Phylogenetics and Evolution. - : Academic Press Inc.. - 1055-7903 .- 1095-9513. ; 195
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Tidskriftsartikel (refereegranskat)abstract
- The global decline of freshwater mussels and their crucial ecological services highlight the need to understand their phylogeny, phylogeography and patterns of genetic diversity to guide conservation efforts. Such knowledge is urgently needed for Unio crassus, a highly imperilled species originally widespread throughout Europe and southwest Asia. Recent studies have resurrected several species from synonymy based on mitochondrial data, revealing U. crassus to be a complex of cryptic species. To address long-standing taxonomic uncertainties hindering effective conservation, we integrate morphometric, phylogenetic, and phylogeographic analyses to examine species diversity within the U. crassus complex across its entire range. Phylogenetic analyses were performed using cytochrome c oxidase subunit I (815 specimens from 182 populations) and, for selected specimens, whole mitogenome sequences and Anchored Hybrid Enrichment (AHE) data on ∼ 600 nuclear loci. Mito-nuclear discordance was detected, consistent with mitochondrial DNA gene flow between some species during the Pliocene and Pleistocene. Fossil-calibrated phylogenies based on AHE data support a Mediterranean origin for the U. crassus complex in the Early Miocene. The results of our integrative approach support 12 species in the group: the previously recognised Unio bruguierianus, Unio carneus, Unio crassus, Unio damascensis, Unio ionicus, Unio sesirmensis, and Unio tumidiformis, and the reinstatement of five nominal taxa: Unio desectus stat. rev., Unio gontierii stat. rev., Unio mardinensis stat. rev., Unio nanus stat. rev., and Unio vicarius stat. rev. Morphometric analyses of shell contours reveal important morphospace overlaps among these species, highlighting cryptic, but geographically structured, diversity. The distribution, taxonomy, phylogeography, and conservation of each species are succinctly described.
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| 8. |
- Persson, Martin, 1971-, et al.
(författare)
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A cross-sectional survey of 5-year-old children with non-syndromic unilateral cleft lip and palate : the Cleft Care UK study. Part 1
- 2015
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Ingår i: Orthod Craniofac Res. - 1601-6343 (Electronic) 1601-6335 (Linking) ; 18 Suppl 2, s. 1-13
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: We describe the methodology for a major study investigating the impact of reconfigured cleft care in the United Kingdom (UK) 15 years after an initial survey, detailed in the Clinical Standards Advisory Group (CSAG) report in 1998, had informed government recommendations on centralization. SETTING AND SAMPLE POPULATION: This is a UK multicentre cross-sectional study of 5-year-olds born with non-syndromic unilateral cleft lip and palate. Children born between 1 April 2005 and 31 March 2007 were seen in cleft centre audit clinics. MATERIALS AND METHODS: Consent was obtained for the collection of routine clinical measures (speech recordings, hearing, photographs, models, oral health, psychosocial factors) and anthropometric measures (height, weight, head circumference). The methodology for each clinical measure followed those of the earlier survey as closely as possible. RESULTS: We identified 359 eligible children and recruited 268 (74.7%) to the study. Eleven separate records for each child were collected at the audit clinics. In total, 2666 (90.4%) were collected from a potential 2948 records. The response rates for the self-reported questionnaires, completed at home, were 52.6% for the Health and Lifestyle Questionnaire and 52.2% for the Satisfaction with Service Questionnaire. CONCLUSIONS: Response rates and measures were similar to those achieved in the previous survey. There are practical, administrative and methodological challenges in repeating cross-sectional surveys 15 years apart and producing comparable data.
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| 9. |
- Ness, A. R., et al.
(författare)
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Centralization of cleft care in the UK. Part 6 : a tale of two studies
- 2015
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Ingår i: Orthod Craniofac Res. - 1601-6343 (Electronic) 1601-6335 (Linking) ; 18 Suppl 2, s. 56-62
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: We summarize and critique the methodology and outcomes from a substantial study which has investigated the impact of reconfigured cleft care in the United Kingdom (UK) 15 years after the UK government started to implement the centralization of cleft care in response to an earlier survey in 1998, the Clinical Standards Advisory Group (CSAG). SETTING AND SAMPLE POPULATION: A UK multicentre cross-sectional study of 5-year-olds born with non-syndromic unilateral cleft lip and palate. Data were collected from children born in the UK with a unilateral cleft lip and palate between 1 April 2005 and 31 March 2007. MATERIALS AND METHODS: We discuss and contextualize the outcomes from speech recordings, hearing, photographs, models, oral health and psychosocial factors in the current study. We refer to the earlier survey and other relevant studies. RESULTS: We present arguments for centralization of cleft care in healthcare systems, and we evidence this with improvements seen over a period of 15 years in the UK. We also make recommendations on how future audit and research may configure. CONCLUSIONS: Outcomes for children with a unilateral cleft lip and palate have improved after the introduction of a centralized multidisciplinary service, and other countries may benefit from this model. Predictors of early outcomes are still needed, and repeated cross-sectional studies, larger longitudinal studies and adequately powered trials are required to create a research-led evidence-based (centralized) service.
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| 10. |
- Bonde, J. P. E., et al.
(författare)
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Occupational risk of COVID-19 across pandemic waves: a two-year national follow-up study of hospital admissions
- 2022
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Ingår i: Scandinavian Journal of Work Environment & Health. - : Scandinavian Journal of Work, Environment and Health. - 0355-3140 .- 1795-990X. ; 48:8, s. 672-677
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Tidskriftsartikel (refereegranskat)abstract
- Objective Assuming that preventive measures to mitigate viral transmission of SARS-CoV-2 at the workplace may have been improved in the course of the COVID-19 pandemic, we examined the occupational risk of COVID-19 related hospital admission across the four pandemic waves in Denmark between week 8, 2020, and week 50, 2021. Methods The study included 4416 cases of COVID-19 related hospital admissions among 2.4 million Danish employees aged 20-69 with follow-up in 2020 through 2021. At-risk industrial sectors and a reference population were defined a priory by a job-exposure matrix on occupational risk for COVID-19. Incidence rate ratios (IRR) and potential effect modification by pandemic wave were computed with Poisson regression adjusted for demographic, social and health factors including completed COVID-19 vaccination. Results We observed an overall elevated relative risk in four of six at-risk industrial sectors, but the pandemic wave only modified the risk among healthcare employees, where the excess risk from a high initial level declined to background levels during the latest waves in models not adjusting for COVID-19 vaccination. In social care, education and transport, the elevated risk was not modified by pandemic wave. Conclusion Danish healthcare employees were to some extent protected against occupational transmission of SARS-CoV-2 during the two last pandemic waves even though the absolute risk conferred by occupation may not have been eliminated. Early vaccination of this group seems not to be the only explanation. The risk in other sectors remained elevated indicating a need to revisit preventive measures.
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| 11. |
- Rando, Halie M, et al.
(författare)
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Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through analysis of Viral Genomics and Structure
- 2021
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world infecting tens of millions of people with coronavirus disease 2019 (COVID-19). While this viral species was unknown prior to January 2020, its similarity to other coronaviruses that infect humans has allowed for rapid insight into the mechanisms that it uses to infect human hosts, as well as the ways in which the human immune system can respond. Here, we contextualize SARS-CoV-2 among other coronaviruses and identify what is known and what can be inferred about its behavior once inside a human host. Because the genomic content of coronaviruses, which specifies the virus's structure, is highly conserved, early genomic analysis provided a significant head start in predicting viral pathogenesis. The pathogenesis of the virus offers insights into symptomatology, transmission, and individual susceptibility. Additionally, prior research into interactions between the human immune system and coronaviruses has identified how these viruses can evade the immune system's protective mechanisms. We also explore systems-level research into the regulatory and proteomic effects of SARS-CoV-2 infection and the immune response. Understanding the structure and behavior of the virus serves to contextualize the many facets of the COVID-19 pandemic and can influence efforts to control the virus and treat the disease.
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| 12. |
- Rando, Halie M, et al.
(författare)
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Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure
- 2021
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Ingår i: mSystems. - 2379-5077. ; 6:5
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Forskningsöversikt (refereegranskat)abstract
- The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions of people with coronavirus disease 2019 (COVID-19). While this viral species was unknown prior to January 2020, its similarity to other coronaviruses that infect humans has allowed for rapid insight into the mechanisms that it uses to infect human hosts, as well as the ways in which the human immune system can respond. Here, we contextualize SARS-CoV-2 among other coronaviruses and identify what is known and what can be inferred about its behavior once inside a human host. Because the genomic content of coronaviruses, which specifies the virus's structure, is highly conserved, early genomic analysis provided a significant head start in predicting viral pathogenesis and in understanding potential differences among variants. The pathogenesis of the virus offers insights into symptomatology, transmission, and individual susceptibility. Additionally, prior research into interactions between the human immune system and coronaviruses has identified how these viruses can evade the immune system's protective mechanisms. We also explore systems-level research into the regulatory and proteomic effects of SARS-CoV-2 infection and the immune response. Understanding the structure and behavior of the virus serves to contextualize the many facets of the COVID-19 pandemic and can influence efforts to control the virus and treat the disease. IMPORTANCE COVID-19 involves a number of organ systems and can present with a wide range of symptoms. From how the virus infects cells to how it spreads between people, the available research suggests that these patterns are very similar to those seen in the closely related viruses SARS-CoV-1 and possibly Middle East respiratory syndrome-related CoV (MERS-CoV). Understanding the pathogenesis of the SARS-CoV-2 virus also contextualizes how the different biological systems affected by COVID-19 connect. Exploring the structure, phylogeny, and pathogenesis of the virus therefore helps to guide interpretation of the broader impacts of the virus on the human body and on human populations. For this reason, an in-depth exploration of viral mechanisms is critical to a robust understanding of SARS-CoV-2 and, potentially, future emergent human CoVs (HCoVs).
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| 16. |
- Lattemann, Martina, 1974-, et al.
(författare)
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Stress reduction in nanocomposite coatings consisting of hexagonal and cubic boron nitride
- 2006
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Ingår i: Surface & Coatings Technology. - : Elsevier BV. - 0257-8972 .- 1879-3347. ; 200:22-23 SPEC. ISS., s. 6459-6464
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Tidskriftsartikel (refereegranskat)abstract
- Cubic boron nitride (c-BN) can be produced by PVD and CVD techniques by intensive ion bombardment leading to highly stressed films. To overcome the problem of highly stressed films, nanocomposite coatings consisting of hexagonal and cubic boron nitride (h-/c-BN) phases have been successfully deposited by reactive rf magnetron sputtering from an h-BN target at a substrate temperature of 350 °C and a dc substrate bias of - 700 V close to the resputtering limit. The morphology of the films was characterized using Fourier transform infrared spectroscopy (FTIR), X-ray diffraction/reflectivity (XRD/XRR) and high-resolution transmission electron microscopy (HRTEM). At low ion energy levels corresponding to low substrate bias values of up to ≈ 200 V pure h-BN was deposited. Higher ion energies led to a strong increase of the c-BN content as well as the residual stress in the films reaching their maximum at ≈ - 300 V substrate bias before decreasing again. Both the c-BN content and the residual stress showed qualitatively the same behaviour with a steeper drop of the residual stress between the maximum and the resputter limit. HRTEM investigation of the films with the maximum densification deposited at a substrate bias of ≈ - 300 V showed an h-BN interlayer growing on the Si substrate with the basal planes perpendicular to the substrate surface on which then almost pure c-BN was identified. The density of these coatings was 3.5 g/cm3 and the residual stress was determined to ≈ - 29 GPa. Depositing boron nitride at a substrate bias of - 700 V, these films comprised a hexagonal interlayer and c-BN in an h-BN matrix on top showing a lower density of 3.2 g/cm3 and a significantly reduced residual stress of - 9 GPa. A further reduction of the residual stress can be achieved by a following heat treatment at 900 °C for 2 h resulting in a value of ≈ - 3 GPa. © 2005 Elsevier B.V. All rights reserved.
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| 19. |
- Tiselius, Peter, 1958, et al.
(författare)
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Functional response of Oikopleura dioica to house clogging due to exposure to algae of different sizes
- 2003
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Ingår i: Marine Biology. - 0025-3162. ; 142:2, s. 253-261
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Tidskriftsartikel (refereegranskat)abstract
- The functional response of the appendicularian Oikopleura dioica was investigated with a unialgal diet (Isochrysis galbana, 0-1,600 mug Cl-1) and with additions of specific concentrations of algae either smaller than the incurrent filter mesh size (Rhodomonas baltica, 90 mug Cl-1; Thalassiosira weissflogii, 60 mug Cl-1) or larger algae (Ceratium lineatum, 8 mug Cl-1; C. tripos, 52 mug C l(-1)). Clearance ranged from 0.13 to 3.3 ml mug C-1 h(-1) and followed a Michaelis-Menten curve corresponding to a maximum filtration rate (particles collected by both animal and house), FRmax = 164 ng C mug C-1 h(-1) and K-m = 64 mug C l(-1). Maximum pellet production was 9 pellets ind(-1) h(-1) and occurred at 100 mugC (-1). Pellet production was proportional to filtration rate below this level, but declined at higher concentrations. House production ranged from 0.5 to 5.5 houses ind(-1) day(-1) and the corresponding curve fit resulted in H-max = 4.6 houses ind(-1) day(-1) and K-m house = 32 mug Cl-1. Addition of edible small algae caused increased internal clogging of the houses, evidenced by significantly higher pigment concentrations in abandoned houses than in houses produced with I.. galbana as a single food. House production was not affected. In contrast, larger algae caused a significantly higher house production, but the algae were not collected on the houses. Increased levels of edible algae will not have negative effects on O. dioica at ecologically realistic concentrations. Ambient bloom concentrations of larger algae may, however, have a negative effect on the growth of O. dioica populations, owing to the compensatory increased house production.
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| 20. |
- Tönnesson, Kajsa, 1971, et al.
(författare)
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Grazing impact of Oikopleura dioica and copepods on an autumn plankton community
- 2005
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Ingår i: Marine Biology Research. - : Informa UK Limited. - 1745-1000 .- 1745-1019. ; 1:5, s. 365-373
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Tidskriftsartikel (refereegranskat)abstract
- Copepods and appendicularians are major grazers in the pelagic environment. They have different retention efficiencies for prey and may therefore exert a variable grazing pressure on the spectrum of pico- to micro-plankton. We determined clearance rates of both groups at one station during 24 h in the Gullmar fjord, west Sweden, in autumn 1999. Total potential prey biomass ranged from 75 mu g C l(-1) at the surface to 14 mu g C l(-1) at 30 m with a dominance of larger dinoflagellates (10-25 mu m athecate species and Gymnodinium /Gyrodinium sp.) and the pennate diatom Pseudo -nitzschia sp. Grazer biomass was dominated by copepods (Acartia clausi, Paracalanus parvus) and appendicularians (Oikopleura dioica). O. dioica showed non-selective clearance rates of 0.7-1.8 ml mu g C-1 h(-1) on most diatoms, flagellates and ciliates, whereas Pseudo -nitzschia sp. and dinoflagellates and ciliates > 25 mu m were not removed by O. dioica. Appendicularian grazing impact was 0.06% d(-1) on the phytoplankton and 0.4% d(-1) on bacterial biomass. Despite a seven-fold higher biomass, the grazing impact of copepods on phytoplankton biomass was only 0.28% d(-1) indicating that O. dioica had a proportionally greater impact and, in contrast to copepods, also utilised bacteria. The low observed grazing impact was due to a low grazer biomass and a prey community largely unavailable to the investigated grazers.
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| 21. |
- Vargas, C. A., et al.
(författare)
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Importance of copepods versus appendicularians in vertical carbon fluxes in a Swedish fjord
- 2002
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Ingår i: Marine Ecology-Progress Series. - 0171-8630. ; 241, s. 125-138
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Tidskriftsartikel (refereegranskat)abstract
- We examined and quantified the contributions of copepods and appendicularians to the vertical flux of carbon during autumn and spring in Gullmar Fjord (west coast of Sweden). Faecal pellet-production rate was determined for major copepod and appendicularian species. In addition, house-production rates were estimated for the appendicularian Oikopleura dioica. Vertical flux of pigments, faecal carbon and appendicularian houses were measured using short-term (24 h) deployments of sediment traps at 2 depths (15 and 30 m). Copepods dominated the community biomass in both spring and autumn and their pellets dominated the faecal carbon flux. O. dioica houses with attached detritus were an important component of the biogenic carbon flux in October (15.3 mg C m(-2) d(-1)), equalling the contribution from copepods at 15 m and 50% of the flux at 30 m. At that time, we observed a loss rate of 70% d(-1) of the houses produced in the water column. In the spring, although Fritillaria borealis dominated the appendicularians, its houses did not appear to contribute to the biogenic flux. Our results suggest that oikopleurids and fritillariids may not operate equivalently in biogeochemical cycles. Because of the significant contribution of appendicularians to carbon fluxes, they should be incorporated in future flow models of coastal oceans.
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